Negative regulatory elements (NRE) region of HIV-1 LTR is involved in down regulation of HIV-1 gene expression. In order to characterize the nature of these NRE sequences, we have sought to determine its role and structure-function relationship with chromatin loop and with nuclear matrix. We find a nuclear matrix attachment region present within NRE of HIV-1 LTR. A sequence specific DNA-binding protein is present in the nuclear matrix that is the attachment site for matrix attachment region sequences. Moreover, we also show that the purified DNA-binding nuclear matrix protein (NMP) specifically expresses the DNA-binding activity of NF-kappaB. The negative effect on NF-kappaB activity due to this MAR- specific interaction provides one mechanism by which the NRE down- regulates HIV gene expression.